RNA 3D Hub //

7NSI Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_7NSI_0011/AA/8:18No text annotation
homologous
HL_4LFB_001
HL_73535.2
HL_7NSI_0081/AA/248:253GNRA variation
geometric
HL_1JID_001
HL_34789.5
HL_7NSI_0231/BA/54:61No text annotation
geometric
HL_4WF9_006
HL_48677.2
HL_7NSI_0241/BA/80:86No text annotation
geometric
HL_5J7L_141
NA
HL_7NSI_0251/BA/121:126GNRA
homologous
HL_7RQB_015
NA
HL_7NSI_0261/BA/167:175No text annotation
geometric
HL_8C3A_039
NA
HL_7NSI_0271/BA/183:192T-loop with 2 stacked bulged bases
homologous
HL_5J7L_150
NA
HL_7NSI_0301/BA/291:300No text annotation
homologous
HL_7RQB_023
NA
HL_7NSI_0311/BA/326:332No text annotation
homologous
HL_7RQB_024
NA
HL_7NSI_0321/BA/372:377No text annotation
homologous
HL_7RQB_025
NA
HL_7NSI_0331/BA/401:410No text annotation
HL_7NSI_0341/BA/442:449GNRA
homologous
HL_4WF9_027
HL_34789.5
HL_7NSI_0351/BA/462:469No text annotation
homologous
HL_5J7L_160
NA
HL_7NSI_0401/BA/688:693No text annotation
geometric
HL_2Y8W_001
HL_40612.1
HL_7NSI_0421/BA/760:767No text annotation
homologous
HL_7RQB_040
NA
HL_7NSI_0431/BA/829:839No text annotation
homologous
HL_5J7L_178
NA
HL_7NSI_0441/BA/850:864No text annotation
HL_7NSI_0471/BA/944:952No text annotation
homologous
HL_7A0S_048
HL_33350.1
HL_7NSI_0481/BA/1022:1031No text annotation
homologous
HL_4WF9_047
HL_78372.2
HL_7NSI_0501/BA/1148:1156LSU P loop
homologous
HL_7A0S_052
HL_11974.3
HL_7NSI_0521/BA/1187:1190No text annotation
geometric
HL_5J7L_176
NA
HL_7NSI_0531/BA/1198:1205GNRA with extra cWW
geometric
HL_4WF9_053
HL_87268.3
HL_7NSI_0551/BA/1294:1302No text annotation
homologous
HL_4WF9_056
HL_52011.2
HL_7NSI_0561/BA/1351:1358GNRA variation
homologous
HL_7A0S_060
HL_46665.3
HL_7NSI_0611/BA/1514:1532No text annotation

Problematic loops

#loop idProblemSequence
HL_7NSI_002No text annotation
HL_7NSI_003No text annotation
HL_7NSI_004No text annotation
HL_7NSI_005No text annotation
HL_7NSI_006No text annotation
HL_7NSI_007GNRA
HL_7NSI_009No text annotation
HL_7NSI_010GNRA
HL_7NSI_011No text annotation
HL_7NSI_012No text annotation
HL_7NSI_013Mini UNCG
HL_7NSI_014No text annotation
HL_7NSI_015Externally structured
HL_7NSI_016Mini UNCG
HL_7NSI_017Pseudoknot geometry
HL_7NSI_018No text annotation
HL_7NSI_019T-loop with 2 stacked bulged bases
HL_7NSI_020No text annotation
HL_7NSI_021No text annotation
HL_7NSI_022GNRA
HL_7NSI_028No text annotation
HL_7NSI_029No text annotation
HL_7NSI_036No text annotation
HL_7NSI_037No text annotation
HL_7NSI_038No text annotation
HL_7NSI_039No text annotation
HL_7NSI_041Mini UNCG
HL_7NSI_045No text annotation
HL_7NSI_046No text annotation
HL_7NSI_049No text annotation
HL_7NSI_051No text annotation
HL_7NSI_054No text annotation
HL_7NSI_057LSU A loop
HL_7NSI_058GNRA
HL_7NSI_059GNRA
HL_7NSI_060No text annotation
HL_7NSI_062No text annotation
HL_7NSI_063tRNA D-loop
HL_7NSI_064tRNA anticodon loop
HL_7NSI_065No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_7NSI_0071/AA/110:115,
1/AA/135:142		Kink-turn with non-sequential stacking
geometric
IL_6CZR_123
NA
IL_7NSI_0161/AA/290:296,
1/AA/484:485		No text annotation
homologous
IL_5J7L_026
NA
IL_7NSI_0231/AA/491:500,
1/AA/507:514		10x8 Sarcin-Ricin; G-bulge
geometric
IL_6UFM_002
IL_22278.1
IL_7NSI_0361/AA/843:845,
1/AA/927:930		No text annotation
geometric
IL_5J7L_058
NA
IL_7NSI_0421/AA/867:870,
1/AA/897:903		No text annotation
IL_7NSI_0441/BA/2:4,
1/BA/147:152		No text annotation
IL_7NSI_0451/BA/4:8,
1/BA/132:147		No text annotation
IL_7NSI_0461/BA/12:13,
1/BA/103:105		Single bulged A
homologous
IL_7A0S_002
IL_14190.3
IL_7NSI_0471/BA/70:73,
1/BA/92:95		Tandem non-canonical cWW pairs
geometric
IL_3R2D_002
IL_71194.3
IL_7NSI_0481/BA/73:79,
1/BA/87:92		7x6 Sarcin-Ricin; G-bulge
geometric
IL_5J7L_251
NA
IL_7NSI_0491/BA/181:183,
1/BA/192:194		Isolated non-canonical cWW pair
geometric
IL_3SZX_001
IL_01003.5
IL_7NSI_0501/BA/214:216,
1/BA/230:232		Isolated non-canonical cWW pair
geometric
IL_3MEI_002
IL_01003.5
IL_7NSI_0511/BA/216:219,
1/BA/226:230		No text annotation
IL_7NSI_0521/BA/240:242,
1/BA/353:355		Isolated non-canonical cWW pair
geometric
IL_7A0S_014
IL_01003.5
IL_7NSI_0531/BA/242:246,
1/BA/346:353		tHW-tHW cross-strand stack
homologous
IL_7RQB_018
NA
IL_7NSI_0541/BA/249:251,
1/BA/341:343		Isolated non-canonical cWW pair
geometric
IL_3GM7_006
IL_01003.5
IL_7NSI_0561/BA/265:266,
1/BA/310:312		Single bulged A
homologous
IL_5J7L_261
NA
IL_7NSI_0581/BA/322:324,
1/BA/334:338		Multiple bulged bases
homologous
IL_5J7L_265
NA
IL_7NSI_0601/BA/478:480,
1/BA/588:589		Single bulged C
homologous
IL_5J7L_276
NA
IL_7NSI_0641/BA/640:647,
1/BA/1006:1012		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
NA
IL_7NSI_0651/BA/663:666,
1/BA/773:779		No text annotation
IL_7NSI_0661/BA/682:687,
1/BA/694:697		C-loop
homologous
IL_7RQB_051
NA
IL_7NSI_0681/BA/719:731,
1/BA/734:737		No text annotation
IL_7NSI_0701/BA/798:800,
1/BA/990:992		Isolated tWW turn
homologous
IL_4WF9_063
IL_10432.2
IL_7NSI_1101/BA/801:809,
1/BA/985:989		No text annotation
homologous
IL_4WF9_117
IL_80252.2
IL_7NSI_0721/BA/804:809,
1/BA/985:988		Intercalated tWH
geometric
IL_4WF9_065
IL_28217.2
IL_7NSI_0731/BA/809:817,
1/BA/982:985		No text annotation
IL_7NSI_0751/BA/873:874,
1/BA/969:971		Single stack bend
geometric
IL_7KGA_003
IL_15011.4
IL_7NSI_0761/BA/880:883,
1/BA/898:899		Minor groove platform, major groove intercalation
homologous
IL_5J7L_314
NA
IL_7NSI_0771/BA/884:885,
1/BA/894:897		Major groove intercalation
homologous
IL_7A0S_067
IL_77710.2
IL_7NSI_0811/BA/1049:1051,
1/BA/1435:1438		No text annotation
homologous
IL_4WF9_079
IL_80025.2
IL_7NSI_0821/BA/1062:1064,
1/BA/1265:1266		Single bulged U
homologous
IL_7RQB_080
NA
IL_7NSI_0831/BA/1065:1066,
1/BA/1261:1264		Minor groove platform
homologous
IL_7RQB_081
NA
IL_7NSI_0841/BA/1075:1078,
1/BA/1138:1140		No text annotation
geometric
IL_4P3T_002
NA
IL_7NSI_1131/BA/1186:1191,
1/BA/1212:1222		No text annotation
IL_7NSI_0891/BA/1276:1277,
1/BA/1321:1323		Single stack bend
geometric
IL_4WF9_089
IL_15011.4
IL_7NSI_0901/BA/1277:1278,
1/BA/1319:1321		Major groove platform
homologous
IL_4WF9_090
IL_48076.9
IL_7NSI_0921/BA/1282:1284,
1/BA/1312:1316		Major groove minor groove platform with extra cWW
homologous
IL_7RQB_094
NA
IL_7NSI_0931/BA/1289:1293,
1/BA/1303:1307		Double sheared with non-canonical cWW
homologous
IL_5J7L_338
NA
IL_7NSI_0971/BA/1344:1346,
1/BA/1363:1367		No text annotation
IL_7NSI_1001/BA/1483:1487,
1/BA/1497:1499		C-loop
geometric
IL_4JRC_003
IL_63596.13

Problematic loops

#loop idProblemSequence
IL_7NSI_001No text annotation
IL_7NSI_002Single bulged A
IL_7NSI_003Single bulged A
IL_7NSI_004Minor groove platform
IL_7NSI_005Minor groove platform
IL_7NSI_006Double sheared with non-canonical cWW
IL_7NSI_008Major groove platform; stack outside cWW
IL_7NSI_104No text annotation
IL_7NSI_009No text annotation
IL_7NSI_010Isolated non-canonical cWW pair
IL_7NSI_011C-loop
IL_7NSI_012Single bulged G
IL_7NSI_013Isolated non-canonical cWW pair
IL_7NSI_014No text annotation
IL_7NSI_015Kink-turn related
IL_7NSI_017UAA/GAN
IL_7NSI_105No text annotation
IL_7NSI_018No text annotation
IL_7NSI_019No text annotation
IL_7NSI_020Other IL
IL_7NSI_021Left turn
IL_7NSI_022tSH-tWH-tHS
IL_7NSI_024Single bulged A
IL_7NSI_025Single bulged G
IL_7NSI_106No text annotation
IL_7NSI_114No text annotation
IL_7NSI_026No text annotation
IL_7NSI_027Minor groove platform
IL_7NSI_107No text annotation
IL_7NSI_028Single bulged U
IL_7NSI_029Isolated cWS basepair
IL_7NSI_030Minor groove platform
IL_7NSI_031Single bulged U
IL_7NSI_032Isolated non-canonical cWW pair
IL_7NSI_033Double sheared
IL_7NSI_034Major groove intercalation
IL_7NSI_035No text annotation
IL_7NSI_037No text annotation
IL_7NSI_038Isolated non-canonical cWW pair
IL_7NSI_039No text annotation
IL_7NSI_040Isolated non-canonical cWW pair
IL_7NSI_041Double sheared
IL_7NSI_043No text annotation
IL_7NSI_055Isolated non-canonical cWW pair
IL_7NSI_057Major groove platform with extra cWW
IL_7NSI_059No text annotation
IL_7NSI_061Isolated non-canonical cWW pair
IL_7NSI_062No text annotation
IL_7NSI_063No text annotation
IL_7NSI_067No text annotation
IL_7NSI_108No text annotation
IL_7NSI_069No text annotation
IL_7NSI_109No text annotation
IL_7NSI_071Major groove platform; stack outside cWW
IL_7NSI_111No text annotation
IL_7NSI_074Single bulged A
IL_7NSI_078Multiple bulged bases
IL_7NSI_079No text annotation
IL_7NSI_080Major groove platform
IL_7NSI_085Isolated non-canonical cWW pair
IL_7NSI_086No text annotation
IL_7NSI_112No text annotation
IL_7NSI_087Minor groove platform with extra cWW
IL_7NSI_088Minor groove platform
IL_7NSI_091No text annotation
IL_7NSI_094Major groove platform
IL_7NSI_095Isolated non-canonical cWW with bulges
IL_7NSI_096No text annotation
IL_7NSI_098Single bulged A
IL_7NSI_0998x7 Sarcin-Ricin; G-bulge
IL_7NSI_101Isolated non-canonical cWW pair
IL_7NSI_102No text annotation
IL_7NSI_103No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_7NSI_0161/BA/8:11,
1/BA/106:120,
1/BA/127:132		No text annotation
J3_7NSI_0171/BA/14:54,
1/BA/61:70,
1/BA/95:102		No text annotation
J3_7NSI_0091/BA/251:257,
1/BA/320:322,
1/BA/338:341		No text annotation
homologous
J3_5J7L_038
NA
J3_7NSI_0181/BA/482:502,
1/BA/526:531,
1/BA/546:586		No text annotation
J3_7NSI_0111/BA/669:676,
1/BA/755:759,
1/BA/768:770		No text annotation
J3_7NSI_0121/BA/676:678,
1/BA/701:708,
1/BA/753:755		No text annotation
J3_7NSI_0191/BA/1182:1183,
1/BA/1225:1236,
1/BA/1245:1251		No text annotation
J3_7NSI_0141/BA/1340:1343,
1/BA/1368:1370,
1/BA/1384:1390		No text annotation
homologous
J3_4WF9_009
J3_32601.6
J4_7NSI_0031/AA/296:298,
1/AA/404:409,
1/AA/450:461,
1/AA/483:484		No text annotation
homologous
J4_5J7L_003
NA
J4_7NSI_0041/BA/648:651,
1/BA/660:661,
1/BA/781:784,
1/BA/1003:1005		No text annotation
J4_7NSI_0051/BA/669:678,
1/BA/701:708,
1/BA/753:759,
1/BA/768:770		No text annotation
J4_7NSI_0061/BA/824:828,
1/BA/840:845,
1/BA/869:874,
1/BA/969:974		No text annotation
J4_7NSI_0071/BA/876:878,
1/BA/901:902,
1/BA/919:928,
1/BA/962:967		No text annotation
homologous
J4_9DFE_008
J4_42306.2
J4_7NSI_0081/BA/1446:1448,
1/BA/1478:1479,
1/BA/1503:1505,
1/BA/1541:1543		No text annotation
J5_7NSI_0041/BA/201:210,
1/BA/236:239,
1/BA/356:359,
1/BA/605:609,
1/BA/624:634		No text annotation
J5_7NSI_0021/BA/1052:1059,
1/BA/1269:1276,
1/BA/1323:1330,
1/BA/1405:1411,
1/BA/1429:1434		No text annotation
J5_7NSI_0031/BA/1069:1072,
1/BA/1143:1146,
1/BA/1158:1159,
1/BA/1181:1182,
1/BA/1251:1258		No text annotation
homologous
J5_7A0S_007
J5_39529.2
J6_7NSI_0011/BA/363:369,
1/BA/380:384,
1/BA/427:434,
1/BA/457:461,
1/BA/470:475,
1/BA/592:601		No text annotation
J6_7NSI_0021/BA/1069:1072,
1/BA/1143:1146,
1/BA/1158:1159,
1/BA/1181:1183,
1/BA/1225:1236,
1/BA/1245:1258		No text annotation

Problematic loops

#loop idProblemSequence
J3_7NSI_001No text annotation
J3_7NSI_002No text annotation
J3_7NSI_003No text annotation
J3_7NSI_015No text annotation
J3_7NSI_004No text annotation
J3_7NSI_005No text annotation
J3_7NSI_006No text annotation
J3_7NSI_007No text annotation
J3_7NSI_008No text annotation
J3_7NSI_010No text annotation
J3_7NSI_013No text annotation
J4_7NSI_001No text annotation
J4_7NSI_002No text annotation
J4_7NSI_009tRNA junction
J5_7NSI_001No text annotation

Coloring options:
Copyright 2026 BGSU RNA group. Page generated in 0.0724 s